Neighbor Optimization RPE¶

This Jupyter notebook (05.02) details the analysis steps to optimize the nearest neighbor analysis.

THIS ANALYSIS STEP DOES NOT OUTPUT AN H5AD FILE.

Initialize Environment¶

First import all the necessary packages here:

InĀ [1]:
# Import necessary packages
import os
import scanpy as sc
import numpy as np
import pandas as pd
import anndata as ad
from datetime import datetime as dt

# Scanpy settings
sc.settings.verbosity = 3
sc.logging.print_header()

# Set working directory
os.chdir("/home/dalbao/2023-012-Runx3mutD8scRNA/AlbaoRunx3Manuscript/single_cell/02_optimization")

adata = "01_25-12-05-17-25_preprocessing_RPE.h5ad"
2025-12-05 22:40:10.192293: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: SSE4.1 SSE4.2 AVX AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
scanpy==1.9.5 anndata==0.10.2 umap==0.5.4 numpy==1.24.4 scipy==1.11.3 pandas==2.1.1 scikit-learn==1.3.1 statsmodels==0.14.0 igraph==0.11.2 louvain==0.8.1 pynndescent==0.5.10

Identify the starting directory. Get a timestamp for the run.

InĀ [2]:
# Determine work location
print("The work location for this notebook is: " + os.getcwd() + "\n")

# Get a timestamp for the start of the run
timestamp = dt.now()
print("This notebook was last run on " + timestamp.strftime("%y-%m-%d %H:%M") + "\n")
The work location for this notebook is: /blue/m.pipkin/dalbao/2023-012-Runx3mutD8scRNA/AlbaoRunx3Manuscript/single_cell/02_optimization

This notebook was last run on 25-12-05 22:40

The work directory is structured to contain a folder named "h5ad" which itself contains output from previous analysis steps. Import data from the latest analysis:

InĀ [3]:
# List items in outs folder
adata = ad.read_h5ad("../../h5ad/" + adata)

# Inspect AnnData
print(adata)
AnnData object with n_obs Ɨ n_vars = 16314 Ɨ 18505
    obs: 'experiment', 'group', 'timepoint', 'infection', 'cell_id', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'doublet_score', 'predicted_doublet', 'scDblFinder_score', 'scDblFinder_class', 'gem', 'QC', 'n_genes', 'S_score', 'G2M_score', 'phase'
    var: 'mt', 'ribo', 'n_cells_by_counts-gem1', 'mean_counts-gem1', 'log1p_mean_counts-gem1', 'pct_dropout_by_counts-gem1', 'total_counts-gem1', 'log1p_total_counts-gem1', 'n_cells_by_counts-gem2', 'mean_counts-gem2', 'log1p_mean_counts-gem2', 'pct_dropout_by_counts-gem2', 'total_counts-gem2', 'log1p_total_counts-gem2', 'n_cells', 'n_counts', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'group_colors', 'hvg', 'log1p', 'pca'
    obsm: 'X_pca'
    varm: 'PCs'
    layers: 'counts', 'soupX_counts'

Optimize Nearest Neighbors¶

Write a function to automate iteration of nearest neighbor analysis:

InĀ [4]:
# Define a function to automate the iteration of different neighbor values, holding PC constant.
def iterate_neighbors(adata_local, pcs = 25, neighbors = 10, min = 0, max = 11):
    # Loop over different nearest neighbor values based on provided min and max values
    for index in range(min, max):
        # Calculate nearest neighbors with n_neighbors of neighbors + index
        adata_mod = sc.pp.neighbors(adata_local, n_neighbors = neighbors + index, n_pcs = pcs, copy = True)
        
        # Do leiden clustering from neighborhood graph
        sc.tl.leiden(adata_mod)
        
        # Initialize the PAGA
        sc.tl.paga(adata_mod)
        sc.pl.paga(adata_mod, title = "neighbor " + str(neighbors + index) + " pcs " + str(pcs))

        # Do a UMAP based on initialized PAGA graph
        sc.tl.umap(adata_mod, init_pos='paga')

        # Plot UMAP annotated by leiden clusters and original identity
        sc.pl.umap(adata_mod, color = "group", title = "neighbor " + str(neighbors + index) + " pcs " + str(pcs))
        sc.pl.umap(adata_mod, color = "leiden", title = "neighbor " + str(neighbors + index) + " pcs " + str(pcs))

        # Get leiden clusters and original identities
        obs_df = sc.get.obs_df(adata_mod, ["group", "leiden"])
        # Print tapply
        print(obs_df.groupby("group").value_counts().unstack())

        del(adata_mod) # Cleanup
        
    # End of loop
    
    del(adata_local)
            
# End of function

25 PCs, neigbhor 3 to 18¶

InĀ [5]:
iterate_neighbors(adata, pcs = 25, neighbors = 3, min = 0, max = 18)
computing neighbors
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:14)
running Leiden clustering
    finished: found 52 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:03)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden    0    1    2    3    4    5    6    7    8    9  ...  42  43  44  45  \
group                                                     ...                   
Base    163  326    1  255  189   18   11  297   18  194  ...  46   4   0  12   
Naive     0    0    0    0    0    0    0    1    0    0  ...   0   1   0   0   
Null    586  230    0  270  401    0    0  154   33  248  ...  11  11   0  10   
WT       41  113  657   59   45  620  595   29   24   40  ...   5   8   0  18   
d5        6   25    5   14    8    7    2   12  430   24  ...   0  37  46   0   
d8       49  104    0   64    9    3    1  111   75   64  ...  32  15   0   6   

leiden  46  47  48  49  50  51  
group                           
Base    18  22   0   0   0   0  
Naive    0   0   0   0   3   0  
Null    14   1   0   0   0   0  
WT       5   4   0   0   0   0  
d5       0   0   9   7   0   3  
d8       4   1   0   0   0   0  

[6 rows x 52 columns]
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 24 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden    0    1     2    3    4     5    6    7    8    9  ...   14   15  \
group                                                       ...             
Base    315  212     8  662  424     0   37  394  342   23  ...  196    7   
Naive     0    0     0    0    0     0    0    1    0    0  ...    0    0   
Null    815  896     1  263  495     0    6  194  318   21  ...   74    1   
WT       67   44  1157  148   89  1096  846   51   58   28  ...   22  519   
d5        3   12     3    7   30     5   12   12    8  647  ...   13   15   
d8      114   29     1   74   89     0    5  172   66   45  ...  304    1   

leiden   16   17   18   19  20  21  22  23  
group                                       
Base      0  194  237  149  24   2   0  20  
Naive   542    0    0    0   0   1   0   0  
Null      0   37   99   60  27  11   0  13  
WT        0  237   20   86  24   8   0   5  
d5        0   15   12    3   0  40  72   0  
d8        0   18   34   23  20  12   0   3  

[6 rows x 24 columns]
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 19 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1     2     3    4    5    6    7    8    9   10   11   12  \
group                                                                        
Base       9  583    20   355  776  506  118  530  387  477   22    0  194   
Naive      0    0     0     0    0    0    0    0    0    1    0  542    0   
Null       2  664     4  1045  330  546  974  299  257  297   19    0   19   
WT      1902  183  1622    78  137   86   52   61   63   77   29    0  303   
d5        10   56    20     5    9    9    4   16   14   23  659    0   13   
d8         1  191     3    74   79  159   17  134  305  147   49    0    6   

leiden   13  14  15  16  17  18  
group                            
Base    165   0   3   2  30  20  
Naive     0   0   0   1   0   0  
Null     57   0   1  11  19  21  
WT      112   0  74   8  18  25  
d5        3  82   2  43   1   0  
d8       25   0   1  13   4   1  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 19 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden    0     1     2    3    4     5    6    7    8    9   10   11   12  \
group                                                                        
Base    743   333     2  665  572     9  545  487   15   16  280   63  215   
Naive     0     0     0    0    0     0    0    1    0    0    0    0    0   
Null    765  1203     0  743  345     3  364  269    3   22   53  468  195   
WT      199    85  1589  121   78  1242   61   76  792   27  381   25   20   
d5       48     4    11    9   16     9   12   19   11  660   19    7    7   
d8      205    92     1   55  391     1   67  141    0   49   19   12  129   

leiden   13   14  15  16  17  18  
group                             
Base      0  196   3   0  33  20  
Naive   542    0   1   0   0   0  
Null      0   84  12   0  18  18  
WT        0   90   8   2  13  21  
d5        0    2  54  79   2   0  
d8        0   29  13   0   4   1  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 17 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1    2     3     4    5    6    7    8    9   10   11   12  \
group                                                                        
Base       4  753  898    93    25  577  534  416  475   18    0  264   86   
Naive      0    0    0     0     0    1    0    0    0    0  542    0    0   
Null       2  835  888  1292     2  310  412  302  336   20    0   95   19   
WT      2327  205  144    63  1290   66  128   71   49   27    0   92  310   
d5        10   66   15     5    22   18    6   20    9  641    0    2   11   
d8         2  215  102    31     1  288  166  259   42   47    0   32    4   

leiden  13  14  15  16  
group                   
Base     5   0  26  23  
Naive    1   0   0   0  
Null    15   0  15  22  
WT       8   2  26  22  
d5      59  85   0   0  
d8      16   0   3   1  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden    0     1     2     3     4    5    6    7    8    9   10   11  12  \
group                                                                        
Base    929   556   555    26     7  800  524  504   20    0  178   45   0   
Naive     0     0     0     0     0    0    1    0    0  542    0    0   0   
Null    872  1259  1251     3     2  476  267   85   37    0   58  206   0   
WT      238    90   103  1887  1793   97   86  375   31    0   85   10   2   
d5       47     9     6    21     8   19   20   23  670    0    2    1  89   
d8      206   143   100     3     2  385  199   26   62    0   24   40   0   

leiden  13  14  15  
group               
Base     3  23  27  
Naive    1   0   0  
Null    11  21  17  
WT       8  21   4  
d5      54   0   0  
d8      12   3   4  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1     2     3     4    5    6    7    8    9   10   11  12  13
group                                                                         
Base     609  974  1018    14     8  391  390  515   23    0  209    3  22  21
Naive      0    0     1     0     0    0    0    0    0  542    0    1   0   0
Null    1681  962   487     3     2  822  367   81   33    0   82   11  20  14
WT       107  305   125  1821  1829   48   63  372   28    0  100    8  20   4
d5         4   38    22    23     8   13   18   23  675    0    3  142   0   0
d8       142  200   395     3     2   50  254   33   86    0   26   12   3   3
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1     2     3    4    5    6    7    8    9   10  11  12  13  \
group                                                                          
Base     789  919    17     9  832  696  598  122   19    0  150   0   3  21   
Naive      0    0     0     0    0    0    1    0    0  542    0   0   1   0   
Null    1425  909     2     3  515  367  300  916   35    0   49   0  12  17   
WT       154  287  1847  1861   97  312   85   46   27    0   84   0   8  18   
d5         9   45    24     8   20   25   16   13  668    0    2  88  51   0   
d8       112  221     3     2  396  172  181   19   63    0   23   0  12   2   

leiden  14  
group       
Base    22  
Naive    0  
Null    15  
WT       4  
d5       0  
d8       3  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4    5    6    7    8    9  10  11  12  13
group                                                                       
Base       8   908  1025  995   516  224   25  185    0  257   0   3  30  21
Naive      0     0     0    0     0    1    0    0  542    0   0   1   0   0
Null       1  1658   900  545  1155   97   39   29    0   97   0  11  17  16
WT      3126   165   301  116    90  488   29  344    0  125   0   8  21  17
d5        21    13    50   20    11   16  670   20    0    5  90  53   0   0
d8         3   136   213  499   176   47   75    9    0   33   0  12   4   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3    4    5    6    7    8    9   10   11  12  13
group                                                                        
Base       7  1409  1196  709   94  438   24   72    0    8  184    4  32  20
Naive      0     0     0    0    0    1    0    0  542    0    0    1   0   0
Null       1  1090  1054  498  902  228   42  624    0    3   77   11  17  18
WT      3128   390   353  111   43   82   49   37    1  469  120    8  21  18
d5        17    24    43   20    2   17  686    5    0   11    2  141   1   0
d8         3   195   209  451   65  144   88   10    0    0   26   12   4   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 12 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4    5    6    7    8    9  10  11
group                                                               
Base      11  1157  1155  838   266  488   23    0  203    3  31  22
Naive      0     0     0    0     0    1    0  542    0    1   0   0
Null       1  1049   812  791  1497  259   41    0   70   11  17  17
WT      3590   330   396  115    72  105   50    0  115    8  27  22
d5        27    46    26   23     4   21  677    0    3  141   1   0
d8         5   224   165  454    93  146   77    0   26   12   4   3
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5    6    7    8    9   10   11  12  \
group                                                                         
Base    1022  1149  1034     8     9  539   26    0  149  183   21    3  23   
Naive      0     0     0     0     0    1    0  542    0    0    0    1   0   
Null    2028  1081   637     2     1  276   45    0   33   79  332   12  22   
WT       179   302   120  2060  1586   89   30    0  318   86   17    8  21   
d5        15    41    26    26     7   15  675    0   15    4    0  144   0   
d8       181   206   498     3     2  167   93    0   11   24    6   12   2   

leiden  13  
group       
Base    31  
Naive    0  
Null    17  
WT      14  
d5       1  
d8       4  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5    6    7    8    9   10  11  12
group                                                                    
Base       6  1000   441  1083  838  537   22    0   32  182    4  28  24
Naive      0     0     0     0    1    0    0  542    0    0    1   0   0
Null       2   962  1739   321  491  533   41    0  362   65   11  15  23
WT      3567   298   106   386  137   97   49    0   13  118    8  28  23
d5        26    42     3    19   25   21  683    0    2    2  144   1   1
d8         3   206   152    82  294  325   95    0    8   26   12   3   3
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3    4    5    6    7    8    9   10  11  12
group                                                                   
Base       6   979  1072  925  796   20    0   38  142  161    3  33  22
Naive      0     0     0    0    1    0  542    0    0    0    1   0   0
Null       1  1939  1076  540  404   35    0  453   18   53   11  17  18
WT      3522   185   294  132  138   31    0   27  332  118    8  22  21
d5        25    10    37   23   25  680    0    5   16    2  145   1   0
d8         4   194   212  359  293   87    0   10    8   24   12   4   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 12 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3    4    5    6    7    8    9  10  11
group                                                              
Base      11   644  1165  857  684  576   21    0  182    3  31  23
Naive      0     0     0    0    1    0    0  542    0    1   0   0
Null       1  2129  1083  701  371  126   38    0   66   11  17  22
WT      3555   137   336  110  124  369   31    0  116    8  22  22
d5        25     9    45   21   23   23  679    0    2  142   0   0
d8         3   197   198  339  311   45   71    0   26   12   4   3
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3    4    5    6    7    8    9   10  11  12
group                                                                   
Base       9  1113   583  833  742  593   18   69    0  176    3  35  23
Naive      0     0     0    0    0    1    0    0  542    0    1   0   0
Null       1  1018  1680  460  363  288   39  597    0   67   11  18  23
WT      3583   346   122   99  320  110   46   31    0  115    8  28  22
d5        25    46     5   25   12   22  683    4    0    2  142   3   0
d8         3   220   172  463   33  188   77   11    0   24   12   4   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1     2    3    4    5    6    7    8    9   10  11  12
group                                                                  
Base       8  840   325  683  802  803  491   23    0  160    3  35  24
Naive      0    0     0    0    0    1    0    0  542    0    1   0   0
Null       2  812  1308  863  597  463  382   39    0   52   11  17  19
WT      3587  312   105  125  269  128   91   45    0  110    8  28  22
d5        25   40     4   17   16   26   17  678    0    2  141   3   0
d8         3  173   121  144   62  298  274   91    0   25   12   4   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 25
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2    3    4     5    6    7    8    9   10  11  12
group                                                                   
Base       9  1027  738  850  667   244  431   23    0  153    3  29  23
Naive      0     0    0    1    0     0    0    0  542    0    1   0   0
Null       1  1210  756  490  637  1041  292   39    0   52   12  17  18
WT      3609   211  274  141  254    64   67   47    0  112    8  21  22
d5        23    25   43   25   17     3   15  676    0    2  140   0   0
d8         4   178  180  294   52    98  281   78    0   26   12   4   2
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())

30 PCs, neigbhor 3 to 18¶

InĀ [6]:
iterate_neighbors(adata, pcs = 30, neighbors = 3, min = 0, max = 18)
computing neighbors
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 50 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:03)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden    0    1    2    3    4    5    6    7    8    9  ...  40  41  42  43  \
group                                                     ...                   
Base    278  164   24  282  289    2  254   12  287  165  ...  55   0  13  19   
Naive     0    0    0    0    1    0    0    0    0    0  ...   0   0   0   0   
Null    297  517    4  173  162    1  275    1  144   84  ...  19   1  12  14   
WT       76   33  623   59   65  604   38  562   96   24  ...   1   0  28   9   
d5       24    1    7   14   18    6    7    6   16    7  ...   1  68   0   0   
d8      120   28    3  114  102    0   23    0   21  262  ...  19   0   1   4   

leiden  44  45  46  47  48  49  
group                           
Base     0   0   0   0   0   0  
Naive    0   0   0   3   0   0  
Null     0   0   0   0   0   0  
WT       0   0   4   0   3   0  
d5      15   5   0   0   0   3  
d8       0   0   0   0   0   0  

[6 rows x 50 columns]
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 27 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden    0     1    2    3    4    5    6    7    8    9  ...   17   18   19  \
group                                                      ...                  
Base    401     8  575    8  225  330  434  355  370    0  ...   71   21  153   
Naive     0     0    0    0    0    0    1    0    0    0  ...    0    0    0   
Null    844     1  285    1  474  293  212  265  247    0  ...  417   39   57   
WT       65  1188   55  942   64  100   54   68  134  773  ...   28   27  118   
d5        6    13    9    5    2   28   17   19   26    0  ...    5  370    3   
d8       50     5   87    0  111  124  148  107   26    0  ...   18   77   24   

leiden   20  21  22  23  24  25  26  
group                                
Base      8  45   3   0  35  18   0  
Naive     0   0   1   0   0   0   0  
Null      4  28  11   0  19  18   0  
WT       19   5   8   0  10  29   0  
d5      299   1  52  69   0   0   4  
d8        4  20  12   0   4   2   0  

[6 rows x 27 columns]
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 22 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3    4    5    6    7    8    9  ...   12   13  \
group                                                        ...             
Base       5   674  653    23  312  447  433  491  309   26  ...    0   56   
Naive      0     0    0     0    0    0    0    0    0    0  ...  542    0   
Null       0  1090  586     2  821  329  453  347   74   49  ...    0  401   
WT      2046   101  200  1380   84   88   47   37  452   36  ...    0   15   
d5        12     8   38    17    7   11    9   12   21  663  ...    0    3   
d8         0    87  165     2  102  119   38   78   23   77  ...    0   19   

leiden   14   15  16  17  18  19  20  21  
group                                     
Base    215    3   4  37   0  19   2   0  
Naive     0    0   1   0   0   0   0   0  
Null     86    1  11  19   0  19   2   0  
WT      105  129   8  13   0  24   9   0  
d5        7    1  61   2  69   0   0   4  
d8       33    2  13   4   0   2   1   0  

[6 rows x 22 columns]
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 17 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1     2    3    4    5     6    7    8    9   10   11   12  \
group                                                                        
Base       6  901   429  619  753  511    25  412   24   88  145    0  226   
Naive      0    0     0    0    0    0     0    1    0    0    0  542    0   
Null       1  848  1289  700  377  347     3  176   44  621   23    0   86   
WT      2369  268   108  102   55   81  1204   45   34   29  381    0  102   
d5        13   47     4   13   11   23    18   13  675    9    9    0    5   
d8         2  176   125   62  107  339     3  224   79   26   11    0   35   

leiden  13  14  15  16  
group                   
Base     3  34   0  21  
Naive    1   0   0   0  
Null    11  17   0  22  
WT       8  20   0  24  
d5      59   0  70   0  
d8      13   5   0   2  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1     2     3    4    5    6    7    8    9   10   11   12  \
group                                                                        
Base       6  951   944   551  521  498   29   26  229    0  142  238    4   
Naive      0    1     0     0    0    0    0    0    0  542    0    0    1   
Null       0  879  1144  1383  359  234    5   45   43    0  339   85   11   
WT      2664  270   146   105   71   45  931   37  377    0   24  104    8   
d5        11   46    15     9   16   10   10  686   10    0   13    2  139   
d8         4  198    93   189  213  333    1   95   15    0   15   34   13   

leiden  13  14  
group           
Base    35  23  
Naive    0   0  
Null    17  21  
WT      22  26  
d5       2   0  
d8       4   2  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4    5    6    7    8    9   10  11  12  13  \
group                                                                           
Base       7  1033   567  848   515  608   27   28  292    0  211   3   0  26   
Naive      0     0     0    0     0    0    0    0    1  542    0   1   0   0   
Null       0   978  1335  556  1246  140    3   43  125    0   88  13   0  21   
WT      2656   294   103   90    95  426  919   54   27    0  113   8   0  24   
d5        14    48    11   22    10   10    9  686   10    0    4  64  80   1   
d8         3   193   201  438    64   32    2   98  133    0   26  13   0   2   

leiden  14  
group       
Base    32  
Naive    0  
Null    17  
WT      21  
d5       0  
d8       4  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3     4    5    6    7    8    9   10   11  12  13
group                                                                         
Base      11  1196  964   592   215  611   23  304    0  214    8    3  26  30
Naive      0     1    0     0     0    0    0    0  542    0    0    1   0   0
Null       2  1006  698  1085  1081  450   43   74    0   74    1   12  22  17
WT      3261   334  111   101    59   53   31  444    0  123  259    8  25  21
d5        20    55   25    15     2    6  689   11    0    3    4  139   0   0
d8         3   262  465    67   103  153   90   16    0   31    0   13   2   4
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5    6    7    8    9  10  11  12
group                                                                   
Base       9   560  1120  1052  888   27  261    0  218    4  27  29   2
Naive      0     0     0     0    0    0    1  542    0    1   0   0   0
Null       1  2077  1021   900  253   44  126    0   85   13  23  16   6
WT      3511   105   321   147  453   50   59    0  129    8  25  22   0
d5        21     8    55    28   12  674   12    0    3  156   0   0   0
d8         3   160   202   483  115  100   99    0   29   13   2   3   0
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5    6    7    8    9   10   11  12  \
group                                                                         
Base       9  1151   804  1001   499   22  310  171    0    6  164    3  28   
Naive      0     0     0     0     0    0    1    0  542    0    0    1   0   
Null       0  1007  1218   685  1361   40  127   24    0    1   53   12  20   
WT      3137   277   133   122   102   32   66  381    0  421  112    8  24   
d5        14    46     9    21    13  682   13   13    0   11    3  143   1   
d8         3   225   114   413   166   99  137    9    0    0   24   13   2   

leiden  13  
group       
Base    29  
Naive    0  
Null    17  
WT      15  
d5       0  
d8       4  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 12 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5    6    7    8    9  10  11
group                                                               
Base       9   729  1220  1110  497   23  372    0  173    3  28  33
Naive      0     0     0     0    0    0    1  542    0    1   0   0
Null       0  2145  1114   888   93   47  157    0   69   11  23  18
WT      3533   122   297   131  467   34   75    0  119    8  24  20
d5        17    10    47    25   17  715   14    0    3  119   2   0
d8         3   188   231   428   59  102  156    0   24   12   2   4
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3    4    5    6    7    8    9   10   11  12  13
group                                                                        
Base    1201     7  978   630  638   12   22  339    0  145  163    3  34  25
Naive      0     0    0     0    0    0    0    1  542    0    0    1   0   0
Null    1009     0  878  1377  985    5   40  150    0   19   52   12  17  21
WT       307  2699  139    98  129  891   30   52    0  342   94    8  19  22
d5        47    12   26    11   10   12  683   11    0   15    3  138   0   1
d8       205     3  463   180   85    0   97  123    0   10   25   12   4   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3     4    5    6    7    8    9   10   11  12  13
group                                                                         
Base       8  1254  991   612   274  480   22  325    0    3  167    3  27  31
Naive      0     0    0     0     0    0    0    1  542    0    0    1   0   0
Null       0  1040  521  1230  1395   84   41  148    0    1   52   12  23  18
WT      3159   338  116    93    70  392   30   67    0  399  110    8  28  20
d5        15    48   21     4    13   19  682   13    0    8    2  143   1   0
d8         2   216  486   154    63   39   98  109    0    0   23   12   3   4
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5    6    7    8    9   10   11  12  13
group                                                                         
Base       8  1202   712   665  921   21    5    0  251  151  198    3  28  32
Naive      0     0     0     0    0    0    0  542    1    0    0    1   0   0
Null       0  1075  1421  1270  498   41    1    0  125   21   57   13  26  17
WT      3027   329   117   127  119   28  537    0   51  321  113    8  33  20
d5        16    47    20     7   20  698    8    0   14   16    4  116   2   1
d8         3   209    51   205  502   94    0    0   89    8   29   12   2   5
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5    6    7    8    9   10   11  12  13
group                                                                         
Base       4  1171   948   245  765  607   15   22  195    0  172    3  24  26
Naive      0     0     0     0    0    1    0    0    0  542    0    1   0   0
Null       1   944  1347  1378  435  287    6   42   23    0   53   12  22  15
WT      2728   312   143    74  106   74  880   32  327    0  109    8  18  19
d5        11    51     9    12   19   15   14  678   15    0    2  141   2   0
d8         2   202   214    39  163  430    0  100   18    0   24   12   2   3
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3    4    5    6    7    8    9   10  11  12
group                                                                   
Base       6  1174  975   522  961  261   19   24    0  197    3  31  24
Naive      0     0    1     0    0    0    0    0  542    0    1   0   0
Null       0   939  583  1406  612  875    6   36    0   58   12  17  21
WT      2762   326  119   100  330   62  943   46    0  102    8  14  18
d5        10    53   26    12   23    2   15  676    0    2  148   1   1
d8         2   203  549    99  111  101    1   95    0   30   12   4   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4    5    6    7    8    9   10  11  12
group                                                                    
Base       8  1191  1061  980   356  307   25   18    0  198    3  24  26
Naive      0     0     0    1     0    0    0    0  542    0    1   0   0
Null       0   933   875  560  1203  837   39    9    0   57   12  23  17
WT      3005   331   307  124    86  101   46  689    0  110    8  18   5
d5        13    48    22   26    12    1  691   12    0    2  140   2   0
d8         2   204   126  550    87   95   96    1    0   29   13   2   4
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5    6    7    8    9   10  11  12
group                                                                    
Base    1101     5  1199   500  986   16   21    0  117  193    3  25  31
Naive      0     0     0     0    1    0    0  542    0    0    1   0   0
Null    1413     0   934  1503  555    4   37    0   11   57   11  23  17
WT       182  2768   305   102  122  829   28    0  338  110    8  24  14
d5        18    12    54    17   23   12  675    0   16    2  139   1   0
d8       156     2   203   154  544    0   93    0    9   30   12   2   4
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 30
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2    3     4     5    6    7    8    9   10  11  12
group                                                                    
Base       9  1141  903  937   535   337   21    0  179   70    3  27  35
Naive      0     0    1    0     0     0    0  542    0    0    1   0   0
Null       0   900  489  812  1179  1024   39    0   59    7   12  25  19
WT      3549   327  131  163    89    91   29    0  117  284    8  28  14
d5        20    52   25   19    10     2  708    0    2   14  116   1   0
d8         2   197  538  107   105   113   95    0   28    6   12   2   4
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())

35 PCs, neigbhor 3 to 18¶

InĀ [7]:
iterate_neighbors(adata, pcs = 35, neighbors = 3, min = 0, max = 18)
computing neighbors
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 46 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden    0    1    2    3    4    5    6    7    8    9  ...  36  37  38  39  \
group                                                     ...                   
Base      9  251  210  301    4  147   18    3  285  148  ...  79   1   1  14   
Naive     0    0    0    0    0    0    0    0    1    0  ...   0   1   0   0   
Null      1  144  395  228    1  318    1    0  158  340  ...  35  11   0  16   
WT      915   38   43   48  678   49  534  551   76   25  ...   9   7   2  26   
d5        9   15   24   12    0    4    5    3    4    6  ...   1  36  61   0   
d8        2  344   70  103    0   82    3    0   17   17  ...   8  11   1   1   

leiden  40  41  42  43  44  45  
group                           
Base    21   0   0   0   0   0  
Naive    0   0   0   4   3   0  
Null    16   0   0   0   0   0  
WT       6  10   0   0   0   2  
d5       0   0   7   0   0   0  
d8       3   0   0   0   0   1  

[6 rows x 46 columns]
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 25 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden    0     1     2    3    4    5    6    7    8    9  ...   15   16  \
group                                                       ...             
Base    617    14     6  528  276  489  158  461  436  125  ...   31    0   
Naive     0     0     0    0    0    1    0    0    0    0  ...    0    0   
Null    678     0     1  291  840  275  757  321  311  625  ...   11    0   
WT      200  1532  1393   96   56   94   38   60   56   41  ...  326  364   
d5       56    10    13   20   11   26    6    7    7   11  ...    7    0   
d8      164     2     1  364   41  154   72  103   89   25  ...    4    0   

leiden   17  18  19  20  21  22  23  24  
group                                    
Base     22  16   1  20   1  28   8   0  
Naive     0   0   0   0   1   0   0   0  
Null      5  73   0  18  11  17   2   0  
WT        4   7   0  29   7  13  13   0  
d5      269   2  74   0  36   0   0   7  
d8        2  18   1   2  11   3   0   0  

[6 rows x 25 columns]
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 18 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1    2     3    4    5    6    7    8    9   10   11   12  13  \
group                                                                           
Base       8  771  575     8  561  711  213  236  618   27  221    0  186   3   
Naive      0    0    0     0    0    1    0    0    0    0    0  542    0   1   
Null       2  793  929     1  378  391  881  788  207   40   32    0   67  11   
WT      2079  174   94  1446  103  108   60   62   79   53  374    0  130   8   
d5        16   41    9    15   19   27   14    2   10  675    6    0    3  58   
d8         1  174   72     1  400  171   57   96   73   99   17    0   31  12   

leiden  14  15  16  17  
group                   
Base    22   0  28   9  
Naive    0   0   0   0  
Null    19   0  17   9  
WT      31   0  15  14  
d5       1  70   3   0  
d8       2   0   3   0  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 17 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1     2     3     4    5    6    7    8    9   10   11  12  \
group                                                                        
Base       7  909   675   411    37  673  589  435   21  198    0  182   3   
Naive      0    0     0     0     0    1    0    0    0    0  542    0   1   
Null       0  852  1064  1118     4  329  644  366   37   44    0   53  11   
WT      2224  230   109    83  1366   78   72   77   32  398    0   89   8   
d5        14   42     6     9    18   20   13   24  673   19    0    3  57   
d8         1  193    96   127     5  329   70  235   88   18    0   29  12   

leiden  13  14  15  16  
group                   
Base    23   0  26   8  
Naive    0   0   0   0  
Null    17   0  17   9  
WT      36   0  15  13  
d5       0  71   0   0  
d8       2   0   4   0  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 17 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2    3     4    5    6    7    8    9   10   11  12  13  \
group                                                                           
Base     657    13  790  797    14  610  399   29  357  262    0  200   3  25   
Naive      0     0    0    0     0    0    0    0    1    0  542    0   1   0   
Null    1196     0  816  483     3  820  789   40  251   46    0   58  11  21   
WT       113  1925  172  100  1678   66   79   34   75  431    0   81   8  39   
d5         9    10   33   27    15   15    6  674   30   16    0    4  57   1   
d8        98     1  136  493     1   84  116   92  125   12    0   32  12   2   

leiden  14  15  16  
group               
Base     0  26  15  
Naive    0   0   0  
Null     0  17  14  
WT       0  15  14  
d5      72   0   0  
d8       0   4   1  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3    4     5    6    7    8    9   10  11  12  13  \
group                                                                           
Base    1069     9  842   346  986    20  305  332   29    0  187   2   0  32   
Naive      0     0    1     0    0     0    0    0    0  542    0   1   0   0   
Null     982     1  453  1355  250     3  791  559   54    0   57  11   0  17   
WT       315  2373  113    82  355  1309   62   31   53    0   79   8   0  15   
d5        53    11   26     4   15    16    6   12  699    0    4  47  75   0   
d8       223     2  508   124  121     0   28   53   99    0   30  12   0   6   

leiden  14  15  
group           
Base    25  13  
Naive    0   0  
Null    20  12  
WT      21  14  
d5       1   0  
d8       2   1  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4    5    6    7    8    9   10  11  12  13  \
group                                                                           
Base       8  1075  1004  910   503  244   26   12    0  150  195   0   2  30   
Naive      0     1     0    0     0    0    0    0  542    0    0   0   1   0   
Null       1   922   898  483  1208  853   38    3    0   33   66   1  11  17   
WT      2849   305   162  123    81   50   27  765    0  299  120   0   8  16   
d5        15    60    13   28    16    2  683   14    0    7    4  87  39   0   
d8         2   219   120  530   147   47   83    0    0   11   30   0  12   5   

leiden  14  15  
group           
Base    24  14  
Naive    0   0  
Null    20  11  
WT      20   5  
d5       1   0  
d8       2   1  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4     5    6    7    8    9   10  11  12  13
group                                                                         
Base    1183   885   628  925    11    12   24  266    0  192    2  24  32  13
Naive      0     0     0    1     0     0    0    0  542    0    1   0   0   0
Null    1038  1533  1258  504     2     2   53   55    0   62   11  21  17   9
WT       308    98   113  112  1920  1707   36  357    0  119    8  24  14  14
d5        49    19     4   25    14    13  702   15    0    4  124   0   0   0
d8       214   155   127  540     1     1   96   25    0   31   12   2   4   1
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5    6    7    8   9  10  11  12  13
group                                                                      
Base       8  1245  1030   627  795   26  184    0  205   3  29   0  30  15
Naive      0     1     0     0    0    0    0  542    0   1   0   0   0   0
Null       2   903  1376  1530  535   44   44    0   65  14  23   0  17  12
WT      3522   324   161   128  107   33  371    0  121   8  26   0  17  12
d5        23    57    13    11   22  683   14    0    4  66   0  76   0   0
d8         2   280   106   186  476   90   16    0   34  13   1   0   4   1
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4    5    6    7    8    9   10  11  12  13
group                                                                        
Base      11  1101   875  823   399  599   19    0  117  180    3  28  30  12
Naive      0     1     0    0     0    0    0  542    0    0    1   0   0   0
Null       2   968  1079  419  1187  725   42    0   28   56   11  22  17   9
WT      3509   322   135  132   112   64   32    0  349  117    8  22  16  12
d5        23    52    13   24     6   13  682    0   13    3  139   1   0   0
d8         2   231   111  510   142   64   89    0   12   28   13   2   4   1
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3    4    5    6    7    8    9   10  11  12  13
group                                                                       
Base       8   891  933   841  627  433   21  212    0  156    3  28  30  14
Naive      0     0    0     0    0    1    0    0  542    0    1   0   0   0
Null       2  1871  860  1111  349  182   46   25    0   54   12  24  17  12
WT      3406   164  291    87  101  204   33  380    0  102    8  24  17  13
d5        18     6   51    16   22   14  681   13    0    3  144   1   0   0
d8         2   190  197    95  469  110   91   13    0   22   13   2   4   1
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5    6    7    8    9   10  11  12  13
group                                                                        
Base       6  1070   959   555  702  478   24  139    0  183    3  26  36  16
Naive      0     1     0     0    0    0    0    0  542    0    1   0   0   0
Null       1   753  1087  1357  373  800   46   25    0   59   12  23  17  12
WT      3461   269   145   129  107   60   34  446    0  116    8  26  16  13
d5        22    53    11     8   21   11  684   17    0    4  137   1   0   0
d8         2   273   113   165  456   58   84    8    0   29   13   2   4   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3    4    5    6    7    8    9   10   11  12  13  \
group                                                                           
Base      10   941   394  792  649  480  599   20    0   82  159    3  25  30   
Naive      0     0     0    0    0    0    1    0  542    0    0    1   0   0   
Null       1  1091  1168  836  344  630  328   41    0   12   54   12  22  17   
WT      3537   156   122   97   96  125  163   33    0  333  108    8  25  15   
d5        23    14     5   16   20   25   53  680    0   14    4  115   0   0   
d8         3    92   145   76  486  110  169   82    0    3   23   13   2   4   

leiden  14  
group       
Base    13  
Naive    0  
Null     9  
WT      12  
d5       0  
d8       1  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1     2     3    4     5    6    7    8    9   10   11  12  \
group                                                                        
Base    1123  935   442    10  819     9  501   21    0   77  182    3  27   
Naive      1    0     0     0    0     0    0    0  542    0    0    1   0   
Null     935  968  1382     1  443     3  665   40    0   10   58   12  22   
WT       281  161   127  2010  113  1589   54   32    0  290  113    8  26   
d5        54   13     9    12   23    13   13  699    0   13    4  116   0   
d8       217   96   145     1  549     1   60   87    0    4   28   13   3   

leiden  13  14  
group           
Base    36  12  
Naive    0   0  
Null    17   9  
WT      14  12  
d5       0   0  
d8       4   1  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 15 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1    2     3    4    5    6    7    8    9   10   11  12  13  \
group                                                                          
Base      11  913  875   418  590  628   20  425    0   87  157    3  28  30   
Naive      0    0    0     0    0    0    0    1  542    0    0    1   0   0   
Null       2  996  792  1299  779  316   44  216    0   10   52   11  22  17   
WT      3551  151  274   119   68   91   31   62    0  309  109    8  28  17   
d5        24   12   40     6   15   20  680   12    0   15    3  141   1   0   
d8         3   99  183   137   70  464   86  121    0    4   23   12   2   4   

leiden  14  
group       
Base    12  
Naive    0  
Null     9  
WT      12  
d5       0  
d8       1  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3    4    5     6    7    8    9   10   11   12  \
group                                                                         
Base     997     4   495  634  655  619    17  478   20    0   58  150    3   
Naive      0     0     0    0    0    0     0    1    0  542    0    0    1   
Null    1350     0  1049  699  730  325     3  242   43    0    8   53   11   
WT       159  2309   147  221   86   86  1322   68   34    0  274   74    8   
d5        12    10    10   57   13   21    16   12  671    0   14    4  128   
d8       111     1   158  135   59  452     1  160   89    0    2   22   12   

leiden  13  14  15  
group               
Base    26  30  11  
Naive    0   0   0  
Null    24  17  11  
WT      24  14   4  
d5       1   0   0  
d8       2   4   1  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5    6    7    8    9  10  11  12
group                                                                   
Base       8  1211  1067   500  961   23  196    0  152    3  27  36  13
Naive      0     0     0     0    1    0    0  542    0    1   0   0   0
Null       2   996  1258  1590  528   43   33    0   54   12  23  17   9
WT      3542   310   133   107  150   31  386    0  108    8  28  15  12
d5        23    56    16     9   26  683   15    0    4  136   1   0   0
d8         2   215   139   154  551   87   15    0   25   13   2   4   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 35
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5    6    7    8    9   10  11  12  13
group                                                                         
Base       8  1089  1116  1063   471   24    0  142  180   23    3  26  36  16
Naive      0     0     0     1     0    0  542    0    0    0    1   0   0   0
Null       1  1376   959   567  1312   41    0   26   59  162   11  23  17  11
WT      3550   153   300   149   128   31    0  348  105    3    8  28  15  12
d5        25    16    55    28    10  700    0   14    4    2  114   1   0   0
d8         2   125   200   574   161   89    0    7   28    2   12   3   4   2
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())

40 PCs, neigbhor 3 to 18¶

InĀ [8]:
iterate_neighbors(adata, pcs = 40, neighbors = 3, min = 0, max = 18)
computing neighbors
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 47 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden    0    1    2    3    4    5    6    7    8    9  ...  37  38  39  40  \
group                                                     ...                   
Base     39  139  350  246  285    8    0    0    0   19  ...  82  48  77  50   
Naive     0    0    0    1    0    0    0    0  542    0  ...   0   0   0   0   
Null      7  504  165  200  226    0    0    0    0   31  ...  21  75  52  26   
WT      749   32   50   94   86  640  592  582    0   31  ...  51  10  13  21   
d5       11    4   13   32   10    8    1    0    0  370  ...  21   7   0   6   
d8        2   48  106  108   73    0    0    0    0   78  ...   2  36  15  26   

leiden  41  42  43  44  45  46  
group                           
Base    32   3  31   1  12   1  
Naive    0   0   0   1   0   0  
Null    54   1  29  11   9   0  
WT      29   1  12   8  11   2  
d5       1  88   2  33   0   0  
d8       7   1   4  12   1   1  

[6 rows x 47 columns]
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 27 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1    2    3     4    5    6    7    8    9  ...   17   18  19  \
group                                                       ...                 
Base       4  320  242  357    17  496    0  480  346  291  ...  119  146  32   
Naive      0    0    0    0     0    1    0    0    0    0  ...    0    0   0   
Null       0  836  720  565     5  286    0  294  231  124  ...   34   61  19   
WT      1485   68   49   83  1016   70  949   38   96   40  ...  261  116  15   
d5        12    7    5   11    19   14    0    7   39   10  ...   34    3   0   
d8         2   48   99   56     4  128    0   55  132  341  ...   12   23   7   

leiden  20  21  22  23  24  25  26  
group                               
Base     0   2   4  35  21  12   0  
Naive    0   1   0   0   0   0   0  
Null     0  11   3  25  14   7   0  
WT       0   8  42   0  24   3   0  
d5      72  36  12   0   0   0   7  
d8       0  12   5   1   1   1   0  

[6 rows x 27 columns]
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 18 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden    0     1     2     3     4    5    6    7    8    9   10   11  12  \
group                                                                        
Base    890   641    11   364    27  556  610  427  380   25    0  196   2   
Naive     0     0     0     0     0    1    0    0    0    0  542    0   1   
Null    832  1181     2  1286     5  518  344   86  139   37    0   81  12   
WT      211   110  1957    83  1630   85   41  401   54   45    0  127   8   
d5       44    12    11     9    13   21   16   18   12  666    0    4  57   
d8      179   117     1   109     3  173   65   50  384   81    0   27  13   

leiden  13  14  15  16  17  
group                       
Base     0  31  22  15   0  
Naive    0   0   0   0   0  
Null     0  16  15  11   0  
WT       0  16  22  30  10  
d5      85   0   1   0   0  
d8       0   4   2   1   0  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 16 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0    1     2     3    4     5    6    7    8    9   10  11  12  13  \
group                                                                           
Base     767  940    11   476  732    16  646   31  268    0  234   2   0  35   
Naive      0    1     0     0    0     0    0    0    0  542    0   1   0   0   
Null    1339  802     0  1064  385     5  738   41   45    0   91  12   0  17   
WT       127  237  2033    87  110  1581   68   32  365    0  130   8   0  16   
d5        11   42     8    10   28    18   13  678   12    0    6  56  86   0   
d8       110  209     1   151  497     1   81   81   16    0   38  14   0   6   

leiden  14  15  
group           
Base    24  15  
Naive    0   0  
Null    15  11  
WT      22  14  
d5       1   0  
d8       2   2  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 17 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4    5    6    7    8    9   10   11  12  \
group                                                                        
Base    1040   655    10  797    15  462  217  440   25    0  325  141   0   
Naive      1     0     0    0     0    0    0    0    0  542    0    0   0   
Null     961  1198     1  438     4  882  734  107   40    0   88   57   0   
WT       260   113  2030  116  1636   56   31  408   31    0   23   64   0   
d5        43     6    10   28    16    5   10   28  692    0    6    3  85   
d8       229   117     2  510     1   60   80   52   84    0   30   23   0   

leiden  13  14  15  16  
group                   
Base    33   1  23  13  
Naive    0   1   0   0  
Null    17  11  15  12  
WT      16   7  26  13  
d5       0  36   1   0  
d8       5  12   2   2  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4     5    6    7    8    9   10  11  12  13
group                                                                         
Base     925  1119   476  894     9     6  451   22    0  220    1  33  24  17
Naive      0     1     0    0     0     0    0    0  542    0    1   0   0   0
Null    1582   864  1349  469     2     2  113   37    0   90   11  17  15  14
WT       136   276    77   98  1807  1793  419   30    0  131    7  16  23  17
d5        14    49    11   23    13    10   24  689    0    4  131   0   1   0
d8       133   208   134  544     2     1   53   82    0   31   12   5   2   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4     5    6    7    8    9   10  11  12  \
group                                                                         
Base     781     9  1065  1078   552    19  439   21    0  166    2  33  23   
Naive      0     0     1     0     0     0    0    0  542    0    1   0   0   
Null    1706     0   912   654  1067     3   76   42    0   52   11  17  15   
WT       143  2627   270   124    87  1036  408   30    0   66    8  16  12   
d5        12    12    49    26    16    12   22  687    0    4  128   0   1   
d8       122     3   233   542   164     0   15   88    0   23   12   5   1   

leiden  13  
group       
Base     9  
Naive    0  
Null    10  
WT       3  
d5       0  
d8       1  
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5    6    7    8    9   10  11  12  13
group                                                                         
Base       7  1063  1070   615   547  598   21   18    0  184    3  32  24  15
Naive      0     1     0     0     0    0    0    0  542    0    1   0   0   0
Null       0   846   636  1385  1409  126   42    3    0   57   12  17  19  13
WT      2997   251   113   122    97  410   29  641    0  113    8  16  18  15
d5        13    53    31     6    14   21  673   13    0    4  140   0   1   0
d8         3   249   529   101   140   52   88    0    0   28   12   4   1   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4     5    6    7    8    9  10  11  12
group                                                                    
Base     904  1132    10  1049  782    20   22    0  200    2  27  33  16
Naive      0     1     0     0    0     0    0  542    0    1   0   0   0
Null    2083  1165     0   673  453     3   42    0   81   11  23  17  14
WT       146   235  2515   118  439  1200   32    0   76    8  32  14  15
d5        13    49    13    31   26    17  687    0    3  130   0   0   0
d8       156   265     3   516  127     0   91    0   29   12   3   5   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5    6    7    8    9  10  11  12
group                                                                   
Base      15  1164  1229   619  760   23    0  140  170    3  35  25  14
Naive      0     0     1     0    0    0  542    0    0    1   0   0   0
Null       0  1876   955  1071  465   47    0   31   59   12  17  19  13
WT      3568   181   290   141  109   32    1  332  116    8  16  23  13
d5        20    10    46    16   23  701    0   16    3  133   0   1   0
d8         3   160   247   164  487   93    0    8   28   12   5   1   1
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 14 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4     5    6    7    8    9   10  11  12  13
group                                                                         
Base    1173  1246   595    14  743     5   21    0  137  186    4  28  35  10
Naive      0     1     0     0    0     0    0  542    0    0    1   0   0   0
Null    1803   907  1192     2  468     0   42    0   31   59   12  22  17  10
WT       175   259   146  2064   97  1609   31    0  307   77    8  31  14  12
d5        13    46    15    18   26     8  692    0   15    4  131   1   0   0
d8       152   251   169     2  493     2   83    0    9   29   12   2   5   0
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3    4    5    6    7    8    9  10  11  12
group                                                                  
Base    1210    14  1280  688  573   23  143    0  189    3  30  32  12
Naive      0     0     1    0    0    0    0  542    0    1   0   0   0
Null    2028     0  1033  992  316   39   32    0   62   11  23  17  12
WT       200  3572   184  177  101   30  395    0  109    8  24  18  12
d5        15    20    38   29   21  687   16    0    3  139   1   0   0
d8       191     2   312  172  376   85   19    0   32   12   2   5   1
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1    2     3    4    5    6    7    8    9  10  11  12
group                                                                  
Base    1159    16  855  1045  737   24    0  143  147    2  27  32  10
Naive      0     0    0     1    0    0  542    0    0    1   0   0   0
Null    2214     0  977   758  434   45    0   28   51   11  20  17  10
WT       192  3624  264   143  101   33    0  332   82    8  25  14  12
d5        11    21   48    24   25  714    0   13    3  109   1   0   0
d8       188     2  179   213  489   89    0    7   23   12   2   5   0
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2    3     4    5    6    7    8    9   10  11  12
group                                                                    
Base    1158  1317     6  950    23  329   22  181    0  147    2  30  32
Naive      0     1     0    0     0    0    0    0  542    0    1   0   0
Null    2238  1165     0  507     4  467   38   43    0   52   11  23  17
WT       199   175  2422  111  1308  110   32  353    0   73    8  25  14
d5        11    30    13   27    15   33  688   19    0    2  130   1   0
d8       217   217     1  514     1  108   86   23    0   23   12   2   5
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 12 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5    6    7    8   9  10  11
group                                                              
Base    1189    15  1465  1076   24  151    0  200    2  28  33  14
Naive      0     0     1     0    0    0  542    0    1   0   0   0
Null    2353     1  1315   684   47   33    0   70   12  22  17  11
WT       211  3573   333   132   33  346    0  120    8  31  18  25
d5        12    19    54    31  697   19    0    3  133   1   0   0
d8       220     2   294   532   94   18    0   29   12   2   5   1
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5    6    7    8    9  10  11  12
group                                                                    
Base    1184  1464  1078    16     2   20  160    0  195    2  27  35  14
Naive      0     1     0     0     0    0    0  542    0    1   0   0   0
Null    2382  1298   668     3     0   47   32    0   73   12  21  17  12
WT       215   336   126  1940  1705   31  329    0   88    8  25  14  13
d5        10    57    27    18     9  694   18    0    4  131   1   0   0
d8       225   290   532     2     0   93   17    0   29   12   2   5   2
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 13 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3     4    5    6    7    8    9   10  11  12
group                                                                     
Base    1106  1260  1046     5    10  349   21  149    0  189    2  25  35
Naive      0     1     0     0     0    0    0    0  542    0    1   0   0
Null    2162  1040   622     0     4  548   44   31    0   64   12  21  17
WT       185   281   131  1838  1813   76   30  343    0   82    8  29  14
d5         9    49    28     8    16    9  699   15    0    4  131   1   0
d8       199   251   528     1     1   89   86    7    0   28   12   3   4
computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
    using 'X_pca' with n_pcs = 40
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
    finished: found 11 clusters and added
    'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
    finished: added
    'paga/connectivities', connectivities adjacency (adata.uns)
    'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
No description has been provided for this image
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(values):
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
No description has been provided for this image
leiden     0     1     2     3    4    5    6    7    8   9  10
group                                                          
Base    1198    15  1471  1103   23  148    0  172    2  29  36
Naive      0     0     1     0    0    0  542    0    1   0   0
Null    2392     1  1313   678   46   28    0   57   12  21  17
WT       216  3604   340   135   32  338    0  114    8  29  14
d5        12    18    60    30  721   18    0    3  107   0   0
d8       227     2   284   543   91   16    0   28   12   1   5
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  print(obs_df.groupby("group").value_counts().unstack())
InĀ [9]:
# End of Notebook
print("\nNotebook Ends")
Notebook Ends